PyBDSF

https://pybdsf.readthedocs.io/en/latest/
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PyBDSF is a tool designed to decompose radio interferometry images into sources and extract their...
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### Get help on process_image task

Source: https://pybdsf.readthedocs.io/en/latest/_sources/ug_basics.rst.txt

Example of getting help on the process_image task.

```text
help process_image
```

--------------------------------

### Get help on rms_box parameter

Source: https://pybdsf.readthedocs.io/en/latest/_sources/ug_basics.rst.txt

Example of getting help on the 'rms_box' parameter.

```text
help 'rms_box'
```

--------------------------------

### Process image with process_image

Source: https://pybdsf.readthedocs.io/en/latest/examples.html

Assumes an image has already been processed with process_image. This is the starting point for the SAMP examples.

```python
BDSF [1]: process_image('VLSS.fits')
...
```

--------------------------------

### Get help on an input parameter

Source: https://pybdsf.readthedocs.io/en/latest/ug_basics.html

Use this command to get help on a specific input parameter. The quotes are necessary because parameter names are strings.

```text
help '<parameter name>'

```

--------------------------------

### Start show_fit with broadcast=True

Source: https://pybdsf.readthedocs.io/en/latest/examples.html

Starts the show_fit task with broadcast=True to highlight the table row corresponding to a source of interest in TOPCAT. The output shows the interactive plot window instructions.

```python
BDSF [6]: show_fit(broadcast=T)
========================================================================
NOTE -- With the mouse pointer in plot window:
  Press "i" ........ : Get integrated flux densities and mean rms
                       values for the visible portion of the image
  Press "m" ........ : Change min and max scaling values
  Press "n" ........ : Show / hide island IDs
  Press "0" ........ : Reset scaling to default
  Click Gaussian ... : Print Gaussian and source IDs (zoom_rect mode,
                       toggled with the "zoom" button and indicated in
                       the lower right corner, must be off)
________________________________________________________________________
```

--------------------------------

### Open FITS file and run source finder (go)

Source: https://pybdsf.readthedocs.io/en/latest/_sources/ug_basics.rst.txt

Interactive PyBDSF session: set the filename, run 'go' to process the image, and observe the detailed output including image properties, background statistics, and the number of sources found.

```text
BDSF [2]: filename = 'sb48.fits'
BDSF [3]: go
--------> go()
--> Opened 'sb48.fits'
Image size .............................. : (256, 256) pixels
Number of channels ...................... : 1
Beam shape (major, minor, pos angle) .... : (0.002916, 0.002654, -173.36) degrees
Frequency of averaged image ............. : 146.497 MHz
Blank pixels in the image ............... : 0 (0.0%)
Flux from sum of (non-blank) pixels ..... : 29.565 Jy
Derived rms_box (box size, step size) ... : (61, 20) pixels
--> Variation in rms image significant
--> Using 2D map for background rms
--> Variation in mean image significant
--> Using 2D map for background mean
Min/max values of background rms map .... : (0.05358, 0.25376) Jy/beam
Min/max values of background mean map ... : (-0.03656, 0.06190) Jy/beam
--> Expected 5-sigma-clipped false detection rate < fdr_ratio
--> Using sigma-clipping thresholding
Number of islands found ................. : 4
Fitting islands with Gaussians .......... : [====] 4/4
Total number of Gaussians fit to image .. : 12
Total flux in model ..................... : 27.336 Jy
Number of sources formed from Gaussians   : 6
```

--------------------------------

### Start PyBDSF interactive shell

Source: https://pybdsf.readthedocs.io/en/latest/_sources/ug_basics.rst.txt

Launch the PyBDSF interactive shell from a terminal. Requires the interactive shell to be installed (not installed by default).

```bash
$ pybdsf
```

--------------------------------

### Start PyBDSF and inspect process_image parameters

Source: https://pybdsf.readthedocs.io/en/latest/_sources/ug_basics.rst.txt

Interactive PyBDSF session showing the startup banner, available commands/tasks, and the parameter list for the process_image task after issuing 'inp process_image'. Use this to see the default values and descriptions for key parameters such as rms_box, thresh_isl, and thresh_pix.

```console
$ pybdsf
PyBDSF version 1.1
========================================================================
PyBDSF commands
  inp task ............ : Set current task and list parameters
  par = val ........... : Set a parameter (par = '' sets it to default)
                          Autocomplete (with TAB) works for par and val
  go .................. : Run the current task
  default ............. : Set current task parameters to default values
  tput ................ : Save parameter values
  tget ................ : Load parameter values
PyBDSF tasks
  process_image ....... : Process an image: find sources, etc.
  show_fit ............ : Show the results of a fit
  write_catalog ....... : Write out list of sources to a file
  export_image ........ : Write residual/model/rms/mean image to a file
PyBDSF help
  help command/task ... : Get help on a command or task
                          (e.g., help process_image)
  help 'par' .......... : Get help on a parameter (e.g., help 'rms_box')
  help changelog ...... : See list of recent changes
________________________________________________________________________

BDSF [1]: inp process_image
--------> inp(process_image)
PROCESS_IMAGE: Find and measure sources in an image.
=================================================================================
filename ................. '': Input image file name
advanced_opts ........ False : Show advanced options
adaptive_rms_box ..... False : Use adaptive rms_box when determining rms and
                                mean maps
atrous_do ............ False : Decompose Gaussian residual image into multiple
                                scales
beam .................. None : FWHM of restoring beam. Specify as (maj, min, pos
                                ang E of N) in degrees. E.g., beam = (0.06, 0.02,
                                13.3). None => get from header
flagging_opts ........ False : Show options for Gaussian flagging
frequency ............. None : Frequency in Hz of input image. E.g., frequency =
                                74e6. None => get from header.
interactive .......... False : Use interactive mode
mean_map .......... 'default': Background mean map: 'default' => calc whether to
                                use or not, 'zero' => 0, 'const' => clipped mean,
                                'map' => use 2-D map
multichan_opts ....... False : Show options for multi-channel images
output_opts .......... False : Show output options
polarisation_do ...... False : Find polarisation properties
psf_vary_do .......... False : Calculate PSF variation across image
rms_box ............... None : Box size, step size for rms/mean map calculation.
                                Specify as (box, step) in pixels. E.g., rms_box =
                                (40, 10) => box of 40x40 pixels, step of 10
                                pixels. None => calculate inside program
rms_map ............... None : Background rms map: True => use 2-D rms map; False
                                => use constant rms; None => calculate inside
                                program
shapelet_do .......... False : Decompose islands into shapelets
spectralindex_do ..... False : Calculate spectral indices (for multi-channel
                                image)
thresh ................ None : Type of thresholding: None => calculate inside
                                program, 'fdr' => use false detection rate
                                algorithm, 'hard' => use sigma clipping
thresh_isl ............. 3.0 : Threshold for the island boundary in number of
                                sigma above the mean. Determines extent of island
                                used for fitting
thresh_pix ............. 5.0 : Source detection threshold: threshold for the
                                island peak in number of sigma above the mean. If
                                false detection rate thresholding is used, this
                                value is ignored and thresh_pix is calculated
                                inside the program
```

--------------------------------

### Gaussian flagging options list (flagging_opts)

Source: https://pybdsf.readthedocs.io/en/latest/process_image.html

Lists the Gaussian flagging options shown when flagging_opts is True. Each line gives the parameter name, its default value, and the condition that triggers a flag. Flag values are summed when multiple conditions are met; for example, a Gaussian too large (64) and too bright (2) gets a final flag of 66.

```text
flagging_opts ......... True : Show options for Gaussian flagging
  flag_bordersize ........ 0 : Flag Gaussian if centre is outside border -
                               flag_bordersize pixels
  flag_maxsize_bm ..... 25.0 : Flag Gaussian if area greater than flag_maxsize_bm
                               times beam area
  flag_maxsize_isl ..... 1.0 : Flag Gaussian if x, y bounding box around
                               sigma-contour is factor times island bbox
  flag_maxsnr .......... 1.5 : Flag Gaussian if peak is greater than flag_maxsnr
                               times max value in island
  flag_minsize_bm ...... 0.7 : Flag Gaussian if flag_smallsrc = True and area
                               smaller than flag_minsize_bm times beam area
  flag_minsnr .......... 0.9 : Flag Gaussian if peak is less than flag_minsnr
                               times thresh_pix times local rms
  flag_smallsrc ...... False : Flag sources smaller than flag_minsize_bm times
                               beam area
```

--------------------------------

### Run process_image and view output

Source: https://pybdsf.readthedocs.io/en/latest/examples.html

Runs the process_image task with 'go'. The output shows image statistics, rms/mean map decisions, island count, and interactive plot instructions.

```text
BDSF [4]: go
---------> go()
--> Opened 'VLSS.fits'
Image size .............................. : (1024, 1024) pixels
Number of channels ...................... : 1
Number of Stokes parameters ............. : 1
Beam shape (major, minor, pos angle) .... : (0.02222, 0.02222, 0.0) degrees
Frequency of image ...................... : 74.000 MHz
Number of blank pixels .................. : 0 (0.0%)
Flux from sum of (non-blank) pixels ..... : 177.465 Jy
Derived rms_box (box size, step size) ... : (196, 65) pixels
--> Variation in rms image significant
--> Using 2D map for background rms
--> Variation in mean image significant
--> Using 2D map for background mean
Min/max values of background rms map .... : (0.06305, 0.16508) Jy/beam
Min/max values of background mean map ... : (-0.01967, 0.01714) Jy/beam
--> Expected 5-sigma-clipped false detection rate < fdr_ratio
--> Using sigma-clipping thresholding
Minimum number of pixels per island ..... : 5
Number of islands found ................. : 115
--> Displaying islands and rms image...
========================================================================
NOTE -- With the mouse pointer in plot window:
  Press "i" ........ : Get integrated fluxes and mean rms values
                       for the visible portion of the image
  Press "m" ........ : Change min and max scaling values
  Press "n" ........ : Show / hide island IDs
  Press "0" ........ : Reset scaling to default
  Click Gaussian ... : Print Gaussian and source IDs (zoom_rect mode,
                       toggled with the "zoom" button and indicated in
                       the lower right corner, must be off)
________________________________________________________________________
```

--------------------------------

### Get help on a command or task

Source: https://pybdsf.readthedocs.io/en/latest/ug_basics.html

Use this command to get help on a PyBDSF command or task. Replace <command or task name> with the actual name, such as process_image.

```text
help <command or task name>

```
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